In low-dose cone beam computed tomography (CT), the insufficient number of photons inevitably results in noise, which reduces the accuracy of disease diagnosis. One approach to improving the image quality of CT images acquired using a low-dose protocol involves the utilization of a reconstruction algorithm that efficiently reduces noise. In this study, we modeled the Feldkamp–Davis–Kress (FDK) algorithm using various filters and projection angles and applied it to the reconstruction process using CT simulation. To quantitatively evaluate the quality of the reconstruction images, we measured the coefficient of variation (COV), and signal-to-noise ratio (SNR) in the air, brain, and bone regions to evaluate the noise level. Furthermore, we calculated root mean square error (RMSE), universal image quality index (UQI), and blind/referenceless image spatial quality evaluator (BRISQUE) as similarity and no-reference evaluation. The Hann filter of the FDK algorithm showed superior performance in terms of COV, SNR, RMSE, and UQI compared to the other filters. In addition, when analyzing the COV and SNR results, we observed that image quality increased significantly at projection angles smaller than approximately 2.8°. Moreover, based on BRISQUE results, we confirm that the Shepp–Logan filter exhibited the most superior performance. In conclusion, we believe that the application of the Hann filter in the FDK reconstruction process offers significant advantages in improving the image quality acquired under a low-dose protocol, and we expect that our study will be a preliminary study of no-reference evaluation of CT reconstruction images.